{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8629CPYB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8629CPYB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0450DIVA](/in-vitro-systems/IGVFSM0450DIVA/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM0450DIVA/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS8629CPYB](/measurement-sets/IGVFDS8629CPYB/) has in progress subobject auxiliary set [IGVFDS8288WJQK](/auxiliary-sets/IGVFDS8288WJQK/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8629CPYB/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8288WJQK](/auxiliary-sets/IGVFDS8288WJQK/) has sequence file(s): [IGVFFI7162NMEV](/sequence-files/IGVFFI7162NMEV/), [IGVFFI2485QHCW](/sequence-files/IGVFFI2485QHCW/), [IGVFFI2651MBBL](/sequence-files/IGVFFI2651MBBL/), [IGVFFI0680QOKE](/sequence-files/IGVFFI0680QOKE/), [IGVFFI4009KRZP](/sequence-files/IGVFFI4009KRZP/), [IGVFFI8994EWVT](/sequence-files/IGVFFI8994EWVT/), [IGVFFI7126BEZG](/sequence-files/IGVFFI7126BEZG/), [IGVFFI7102LRYO](/sequence-files/IGVFFI7102LRYO/), [IGVFFI6520TEPW](/sequence-files/IGVFFI6520TEPW/), [IGVFFI9885WAYR](/sequence-files/IGVFFI9885WAYR/), [IGVFFI4326RSEE](/sequence-files/IGVFFI4326RSEE/), [IGVFFI7634THJL](/sequence-files/IGVFFI7634THJL/), [IGVFFI6643RXYS](/sequence-files/IGVFFI6643RXYS/), [IGVFFI4233IDKO](/sequence-files/IGVFFI4233IDKO/), [IGVFFI0937JKTX](/sequence-files/IGVFFI0937JKTX/), [IGVFFI8835LGFN](/sequence-files/IGVFFI8835LGFN/), [IGVFFI8388ENWV](/sequence-files/IGVFFI8388ENWV/), [IGVFFI8695EBLD](/sequence-files/IGVFFI8695EBLD/), [IGVFFI7807UKYJ](/sequence-files/IGVFFI7807UKYJ/), [IGVFFI0604FIKB](/sequence-files/IGVFFI0604FIKB/), [IGVFFI6127EKXN](/sequence-files/IGVFFI6127EKXN/), [IGVFFI6452YQQQ](/sequence-files/IGVFFI6452YQQQ/), [IGVFFI3395SYDN](/sequence-files/IGVFFI3395SYDN/), [IGVFFI5369CUSP](/sequence-files/IGVFFI5369CUSP/), [IGVFFI7660XDAA](/sequence-files/IGVFFI7660XDAA/), [IGVFFI5129FTIF](/sequence-files/IGVFFI5129FTIF/), [IGVFFI4723JMWA](/sequence-files/IGVFFI4723JMWA/), [IGVFFI4219BQNZ](/sequence-files/IGVFFI4219BQNZ/), [IGVFFI7844RDQK](/sequence-files/IGVFFI7844RDQK/), [IGVFFI1286NYQN](/sequence-files/IGVFFI1286NYQN/), [IGVFFI1019IHWR](/sequence-files/IGVFFI1019IHWR/), [IGVFFI1671NGBR](/sequence-files/IGVFFI1671NGBR/), [IGVFFI6132IGDK](/sequence-files/IGVFFI6132IGDK/), [IGVFFI2621TQRQ](/sequence-files/IGVFFI2621TQRQ/), [IGVFFI4238ROJZ](/sequence-files/IGVFFI4238ROJZ/), [IGVFFI6805RFPJ](/sequence-files/IGVFFI6805RFPJ/), [IGVFFI6297TFMW](/sequence-files/IGVFFI6297TFMW/), [IGVFFI0161OWBW](/sequence-files/IGVFFI0161OWBW/), [IGVFFI4206IKEE](/sequence-files/IGVFFI4206IKEE/), [IGVFFI9325LKZS](/sequence-files/IGVFFI9325LKZS/), [IGVFFI9851JPHD](/sequence-files/IGVFFI9851JPHD/), [IGVFFI3273CLCU](/sequence-files/IGVFFI3273CLCU/), [IGVFFI2530EQUG](/sequence-files/IGVFFI2530EQUG/), [IGVFFI3854ANZB](/sequence-files/IGVFFI3854ANZB/), [IGVFFI3022SAZV](/sequence-files/IGVFFI3022SAZV/), [IGVFFI0088UADS](/sequence-files/IGVFFI0088UADS/), [IGVFFI4532XBOH](/sequence-files/IGVFFI4532XBOH/), [IGVFFI9104WBGE](/sequence-files/IGVFFI9104WBGE/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS8288WJQK/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8629CPYB](/measurement-sets/IGVFDS8629CPYB/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS8629CPYB/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8288WJQK](/auxiliary-sets/IGVFDS8288WJQK/) has sequence file(s) [IGVFFI7162NMEV](/sequence-files/IGVFFI7162NMEV/), [IGVFFI2485QHCW](/sequence-files/IGVFFI2485QHCW/), [IGVFFI2651MBBL](/sequence-files/IGVFFI2651MBBL/), [IGVFFI0680QOKE](/sequence-files/IGVFFI0680QOKE/), [IGVFFI4009KRZP](/sequence-files/IGVFFI4009KRZP/), [IGVFFI8994EWVT](/sequence-files/IGVFFI8994EWVT/), [IGVFFI7126BEZG](/sequence-files/IGVFFI7126BEZG/), [IGVFFI7102LRYO](/sequence-files/IGVFFI7102LRYO/), [IGVFFI6520TEPW](/sequence-files/IGVFFI6520TEPW/), [IGVFFI9885WAYR](/sequence-files/IGVFFI9885WAYR/), [IGVFFI4326RSEE](/sequence-files/IGVFFI4326RSEE/), [IGVFFI7634THJL](/sequence-files/IGVFFI7634THJL/), [IGVFFI6643RXYS](/sequence-files/IGVFFI6643RXYS/), [IGVFFI4233IDKO](/sequence-files/IGVFFI4233IDKO/), [IGVFFI0937JKTX](/sequence-files/IGVFFI0937JKTX/), [IGVFFI8835LGFN](/sequence-files/IGVFFI8835LGFN/), [IGVFFI8388ENWV](/sequence-files/IGVFFI8388ENWV/), [IGVFFI8695EBLD](/sequence-files/IGVFFI8695EBLD/), [IGVFFI7807UKYJ](/sequence-files/IGVFFI7807UKYJ/), [IGVFFI0604FIKB](/sequence-files/IGVFFI0604FIKB/), [IGVFFI6127EKXN](/sequence-files/IGVFFI6127EKXN/), [IGVFFI6452YQQQ](/sequence-files/IGVFFI6452YQQQ/), [IGVFFI3395SYDN](/sequence-files/IGVFFI3395SYDN/), [IGVFFI5369CUSP](/sequence-files/IGVFFI5369CUSP/), [IGVFFI7660XDAA](/sequence-files/IGVFFI7660XDAA/), [IGVFFI5129FTIF](/sequence-files/IGVFFI5129FTIF/), [IGVFFI4723JMWA](/sequence-files/IGVFFI4723JMWA/), [IGVFFI4219BQNZ](/sequence-files/IGVFFI4219BQNZ/), [IGVFFI7844RDQK](/sequence-files/IGVFFI7844RDQK/), [IGVFFI1286NYQN](/sequence-files/IGVFFI1286NYQN/), [IGVFFI1019IHWR](/sequence-files/IGVFFI1019IHWR/), [IGVFFI1671NGBR](/sequence-files/IGVFFI1671NGBR/), [IGVFFI6132IGDK](/sequence-files/IGVFFI6132IGDK/), [IGVFFI2621TQRQ](/sequence-files/IGVFFI2621TQRQ/), [IGVFFI4238ROJZ](/sequence-files/IGVFFI4238ROJZ/), [IGVFFI6805RFPJ](/sequence-files/IGVFFI6805RFPJ/), [IGVFFI6297TFMW](/sequence-files/IGVFFI6297TFMW/), [IGVFFI0161OWBW](/sequence-files/IGVFFI0161OWBW/), [IGVFFI4206IKEE](/sequence-files/IGVFFI4206IKEE/), [IGVFFI9325LKZS](/sequence-files/IGVFFI9325LKZS/), [IGVFFI9851JPHD](/sequence-files/IGVFFI9851JPHD/), [IGVFFI3273CLCU](/sequence-files/IGVFFI3273CLCU/), [IGVFFI2530EQUG](/sequence-files/IGVFFI2530EQUG/), [IGVFFI3854ANZB](/sequence-files/IGVFFI3854ANZB/), [IGVFFI3022SAZV](/sequence-files/IGVFFI3022SAZV/), [IGVFFI0088UADS](/sequence-files/IGVFFI0088UADS/), [IGVFFI4532XBOH](/sequence-files/IGVFFI4532XBOH/), [IGVFFI9104WBGE](/sequence-files/IGVFFI9104WBGE/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS8288WJQK/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8288WJQK](/auxiliary-sets/IGVFDS8288WJQK/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS8288WJQK/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8288WJQK/",
"accession": "IGVFDS8288WJQK",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC_AmpliconSequencing_AuxiliarySet"
],
"file_set_type": "variant sequencing"
}
],
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:11.677675+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/IGVFDS5031MNRR/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "Variant FlowFISH",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:05:31.732823+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0450DIVA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0450DIVA",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2374NXLW/",
"accession": "IGVFDS2374NXLW",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 51-75% expression of PPIF) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "21",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T22:05:55.704308+00:00",
"summary": "Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"symbol": "PPIF",
"synonyms": [
"rotamase F",
"CYP3",
"cyclophilin F",
"mitochondrial cyclophilin",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"CypD",
"Cyp-D",
"cyclophilin 3",
"cyclophilin D",
"CyP-M",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIase F"
]
}
],
"uuid": "041a55b3-5702-4de8-b888-c3f66535ee9f"
}